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diff beta_diversity_through_3d_plots.xml @ 0:e5c3175506b7 default tip

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Initial tool configs for qiime, most need work.
author Jim Johnson <jj@umn.edu>
date Sun, 17 Jul 2011 10:30:11 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/beta_diversity_through_3d_plots.xml	Sun Jul 17 10:30:11 2011 -0500
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+<tool id="beta_diversity_through_3d_plots" name="beta_diversity_through_3d_plots" version="1.2.0">
+ <description>A workflow script for computing beta diversity distance matrices and the corresponding 3D plots</description>
+ <requirements>
+  <requirement type="binary">beta_diversity_through_3d_plots.py</requirement>
+ </requirements>
+ <command interpreter="python">
+  qiime_wrapper.py
+  --galaxy_outputdir='$log.extra_files_path'
+  --galaxy_datasets='^log_\S+\.txt$:'$log,'^prefs\.txt$:'$prefs
+  beta_diversity_through_3d_plots.py
+  --otu_table_fp=$otu_table_fp
+  --mapping_fp=$mapping_fp
+  --output_dir='$log.extra_files_path'
+  --force
+  #if $parameter.source == 'hist':
+   --parameter_fp=$parameter_fp
+  #else:
+   --parameter_fp=$parameter_generated
+  #end if
+  --tree_fp=$tree_fp
+  #if int($seqs_per_sample) > 0:
+   --seqs_per_sample=$seqs_per_sample
+  #end if
+  $parallel
+ </command>
+ <inputs>
+  <param name="otu_table_fp" type="data" format="qiimeotutable" label="otu_table_fp"
+   help="the input OTU table [REQUIRED]"/>
+  <param name="mapping_fp" type="data" format="qiimemapping" label="mapping_fp"
+   help="path to the mapping file [REQUIRED]"/>
+
+  <conditional name="parameter">
+   <param name="source" type="select" label="Parameters from" help="">
+    <option value="hist">Your History</option>
+    <option value="build">Build a Parameter file</option>
+   </param>
+   <when value="hist">
+    <param name="parameter_fp" type="data" format="qiimeparams" label="parameter_fp"
+     help="path to the parameter file [REQUIRED]"/>
+   </when> <!-- hist -->
+   <when value="build">
+   <!--
+     beta_diversity:metrics
+        params['alpha_diversity']['metrics'].split(',')
+        params['multiple_rarefactions']
+        params['parallel'])
+        params['alpha_diversity'])
+        params['collate_alpha']
+        params['make_rarefaction_plots']
+    multiple_rarefactions.py
+     min seqs/sample
+     max seqs/sample
+     step
+     depth    sequences per sample to subsample
+     num-reps
+     lineages_included 
+     keep_empty_otus
+    alpha_diversity.py
+    collate_alpha.py
+    make_rarefaction_plots.py
+   -->
+   </when> <!-- build -->
+  </conditional> <!-- parameter -->
+  <param name="tree_fp" type="data" format="tre" optional="true" label="tree_fp"
+   help="path to the tree file [default: ('NO', 'DEFAULT'); REQUIRED for phylogenetic measures]"/>
+  <param name="seqs_per_sample" type="integer" value="-1" label="seqs_per_sample"
+   help="depth of coverage for even sampling [default: ('NO', 'DEFAULT')]"/>
+  <param name="parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="false" label="parallel"
+   help="Run in parallel where available [default: False]"/>
+ </inputs>
+ <configfiles>
+  <configfile name="parameter_generated">
+beta_diversity:metrics
+alpha_diversity:metrics	chao1,observed_species,PD_whole_tree
+multiple_rarefactions_even_depth:num-reps	20
+parallel:jobs_to_start	2
+parallel:retain_temp_files	False
+parallel:seconds_to_sleep	60
+collate_alpha:example_path
+make_rarefaction_plots:imagetype	png
+make_rarefaction_plots:resolution	75
+make_rarefaction_plots:background_color	white
+make_rarefaction_plots:prefs_path
+  </configfile>
+  <configfile name="output_template">
+<![CDATA[
+<html>
+<body>
+<!-- plots discrete/continuous for each beta_diversiry metric txt_3D.html -->
+<a href="rarefaction_plots.html">rarefaction_plots.html</a>
+</body>
+</html>
+]]>
+  </configfile>
+
+ </configfiles>
+ <outputs>
+  <!--
+This script results in a distance matrix (from beta_diversity.py), 
+a principal coordinates file (from principal_coordinates.py), 
+a preferences file (from make_prefs_file.py) 
+and folder containing the resulting 3d PCoA plots (as an html from make_3d_plots.py).
+   -->
+  <data format="txt" name="log" label="${tool.name} on ${on_string}: log"/>
+  <data format="qiimedistmat" name="seqs_otu_table" label="${tool.name} on ${on_string}: weighted_unifrac_seqs_otu_table_even146.txt"/>
+                 {weighted_unifrac}_{dataset_4477.dat}
+  <data format="qiimepca" name="pca" label="${tool.name} on ${on_string}: weighted_unifrac_pc.txt"/>
+                 
+  <data format="qiimeprefs" name="prefs" label="${tool.name} on ${on_string}: prefs.txt"/>
+  <data format="html" name="pc_plots" label="${tool.name} on ${on_string}: PCoA plots"/>
+ </outputs>
+ <tests>
+ </tests>
+ <help>
+$ beta_diversity_through_3d_plots.py -i wf_da/uclust_picked_otus/rep_set/rdp_assigned_taxonomy/otu_table/seqs_otu_table.txt -m Fasting_Map.txt -o wf_bdiv_even146_test/  -p custom_parameters.tt -t wf_da/uclust_picked_otus/rep_set/pynast_aligned_seqs/fasttree_phylogeny/seqs_rep_set.tre -e 146 --print_only
+
+single_rarefaction.py -i wf_da/uclust_picked_otus/rep_set/rdp_assigned_taxonomy/otu_table/seqs_otu_table.txt -o wf_bdiv_even146_test//seqs_otu_table_even146.txt -d 146
+make_prefs_file.py -m Fasting_Map.txt -o wf_bdiv_even146_test//prefs.txt --monte_carlo_dists 10 --background_color black --mapping_headers_to_use Treatment,DOB
+beta_diversity.py -i wf_bdiv_even146_test//seqs_otu_table_even146.txt -o wf_bdiv_even146_test/ --metrics weighted_unifrac  -t wf_da/uclust_picked_otus/rep_set/pynast_aligned_seqs/fasttree_phylogeny/seqs_rep_set.tre 
+principal_coordinates.py -i wf_bdiv_even146_test//weighted_unifrac_seqs_otu_table_even146.txt -o wf_bdiv_even146_test//weighted_unifrac_pc.txt 
+make_3d_plots.py -p wf_bdiv_even146_test//prefs.txt -i wf_bdiv_even146_test//weighted_unifrac_pc.txt -o wf_bdiv_even146_test//weighted_unifrac_3d_continuous/ -m Fasting_Map.txt --ellipsoid_smoothness 1
+make_3d_plots.py -b "SampleID,BarcodeSequence,LinkerPrimerSequence,Treatment,DOB,Description" -i wf_bdiv_even146_test//weighted_unifrac_pc.txt -o wf_bdiv_even146_test//weighted_unifrac_3d_discrete/ -m Fasting_Map.txt --ellipsoid_smoothness 1
+beta_diversity.py -i wf_bdiv_even146_test//seqs_otu_table_even146.txt -o wf_bdiv_even146_test/ --metrics unweighted_unifrac  -t wf_da/uclust_picked_otus/rep_set/pynast_aligned_seqs/fasttree_phylogeny/seqs_rep_set.tre 
+principal_coordinates.py -i wf_bdiv_even146_test//unweighted_unifrac_seqs_otu_table_even146.txt -o wf_bdiv_even146_test//unweighted_unifrac_pc.txt 
+make_3d_plots.py -p wf_bdiv_even146_test//prefs.txt -i wf_bdiv_even146_test//unweighted_unifrac_pc.txt -o wf_bdiv_even146_test//unweighted_unifrac_3d_continuous/ -m Fasting_Map.txt --ellipsoid_smoothness 1
+make_3d_plots.py -b "SampleID,BarcodeSequence,LinkerPrimerSequence,Treatment,DOB,Description" -i wf_bdiv_even146_test//unweighted_unifrac_pc.txt -o wf_bdiv_even146_test//unweighted_unifrac_3d_discrete/ -m Fasting_Map.txt --ellipsoid_smoothness 1
+
+  
+ </help>
+</tool>
+